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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttaatttcttgattgccaaatgtaagcaaaatgtttgtagcagttgattgcagctacaaatgaagttactcattatgctcccttttaaacgttttgcagTTCTTCATCTTGCTTTCCTGCTCCCTGGCCGTCTTCTGCAACATGAGCCAATACCTCTGCATCGGCCGGTTCTCAGCGACCTCGTTTCAGGTCCTGGGCC

Basic information

species Zea mays
transcript GRMZM2G055216_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G055216_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os07g39280.1 (Oryza sativa), 3'ss of exon 4
cttaatttcttgattgccaaatgtaagcaaaatgtttgtagcagttgattgcagctacaaatgaagttactcattatgctcccttttaaacgttttgcagTTCTTCATCTTGCTTTCCTGCTCCCTGGCCGTCTTCTGCAACATGAGCCAATACCTCTGCATCGGCCGGTTCTCAGCGACCTCGTTTCAGGTCCTGGGCC
  |  |||  | |||    | |            |||    |   |  | | |  |   ||   |  | || |  |    |  | ||||    | ||||||||||||| |||||||| |||||| |||| |||||||||||||||||||| ||||||||||||||||||||||| || || ||||| |||||||||||||
tctgttttaatcattatgcacttctccttgttgctttaatactcctactgggaattcttaaaacatgttctaacaacttgctatgttaataactctgcagTTCTTCATATTGCTTTCTTGCTCCTTGGCTGTCTTCTGCAACATGAGCCAGTACCTCTGCATCGGCCGGTTCTCTGCAACTTCGTTCCAGGTCCTGGGCC

upper sequence: GRMZM2G055216_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT1G76670.1 (Arabidopsis thaliana), 3'ss of exon 4
cttaatttcttgattgccaaatgtaagcaaaatgtttgtagcagttgattgcagctacaaatgaagttactcattatgctcccttttaaacgttttgcagTTCTTCATCTTGCTTTCCTGCTCCCTGGCCGTCTTCTGCAACATGAGCCAATACCTCTGCATCGGCCGGTTCTCAGCGACCTCGTTTCAGGTCCTGGGCC
             |    ||||          | | ||   ||| ||| | ||     |||   |   | || |||   |   | |   |  |||||||||||| |||  | || |||||  |  | ||||| ||||| ||||| |||||||| |||||||||||  | ||||||||||| || || || || || ||||
------------gtaagtaaattctcaagttctctatgattcagatgact-caaacgtaaacacaa--aatctttactttttatctctcat-ttttgcagTTCTGCATTCTTCTCTCCTGTGCATTAGCCGTTTTCTGTAACATAAGCCAATATCTCTGCATCGGAAGATTCTCAGCGACATCTTTCCAAGTTCTAGGCC

upper sequence: GRMZM2G055216_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv18s0122g00090.t01 (Vitis vinifera), 3'ss of exon 4
cttaatttcttgattgccaaatgtaagcaaaatgtttgtagcagt--tgattgcagctacaaatga--agt---tactcatta-----tgctccctt--ttaaacgttttgcagTTCTTCATCTTGCTTTCCTGCTCCCTGGCCGTCTTCTGCAACATGAGCCAATACCTCTGCATCGGCCGGTTCTCAGCGACCTCGTTTCAGGTCCTGGGCC
  |||   ||| ||      ||| |   |  || | |   | | |  |||   |||| ||| || |  |||   ||   ||       ||||  |||  |  || | | ||||||| |||||  | ||||| |||||||| || || ||||||||  ||||||| ||||||||||| || || ||||||||    || || |||||  | || |
-gtaagaactt-atctttctatgcatatattatttctaatggattactgagcacagccacatattatcagtctgtatagatagattcctgctaacttaatccaatggtgtgcagTTTTTCATACTCCTTTCATGCTCCCTAGCAGTGTTCTGCAATGTGAGCCAGTACCTCTGCATAGGACGCTTCTCAGCAGTTTCCTTCCAGGTTTTAGGTC

upper sequence: GRMZM2G055216_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S15_387V6.1 (Physcomitrella patens), 3'ss of exon 5
cttaatttcttgattgccaaatgtaagcaaaatgtttgtagcagttgattgcagctacaaatgaagttactcattatgctccctt-ttaaacgttttgcagTTCTTCATCTTGCTTTCCTGCTCCCTGGCCGTCTTCTGCAACATGAGCCAATACCTCTGCATCGGCCGGTTCTCAGCGACCTCGTTTCAGGTCCTGGGCC
 || ||| |||   ||   |    |   |  ||||     |   ||     | ||||    |  |  | |       |||   || |   |   | |||||||||| ||  | ||||| ||  | || || || ||||||||| ||||||| ||| | ||||||||||||||||| ||     | ||||||          
gttcattcctttcctggggagaaaatctagcatgtgaagtgggtttctgctctgctattgtttga-ctgcaagcggagcttgtttatcgtatcatgtgcagTTCTTTATACTTCTTTCGTGTACACTAGCGGTGTTCTGCAACGTGAGCCAGTACTTGTGCATCGGCCGGTTCTCCGCTGTGACATTTCAG----------

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|149023508|gb|EE045856.2|EE045856
EST:     ATCTAAATGGACGGTCATTGTTGAACTACCCTTTTTCGGGAGGGGCAACT                         TTCTTCATCTTGCTTTCCTGCTCCCT
genomic: ATCTAAATGGACGGTCATTGTTGAACTACCCTTTTTCGGGAGGGGCAACTgtaagttatc ... cgttttgcagTTCTTCATCTTGCTTTCCTGCTCCCT
EST: gi|74233833|gb|DT641747.1|DT641747
EST:     ATCTAAATGGACGGTCATTGTTGAACTACCCTTTTTCGGGAGGGGCAACT                         TTCTTCATCTTGCTTTCCTGCTCCCTGGCCGTCTTCTGCAACATGAGCCAA
genomic: ATCTAAATGGACGGTCATTGTTGAACTACCCTTTTTCGGGAGGGGCAACTgtaagttatc ... cgttttgcagTTCTTCATCTTGCTTTCCTGCTCCCTGGCCGTCTTCTGCAACATGAGCCAA
EST: gi|91872782|gb|EB402739.1|EB402739
EST:     ATCTAAATGGACGGTCATTGTTGAACTACCCTTTTTCGGGAGGGGCAACT                         TTCTTCATCTTGCTTTCCTGCTCCCTGGCCGTCTTCTGCAACATGAGCC
genomic: ATCTAAATGGACGGTCATTGTTGAACTACCCTTTTTCGGGAGGGGCAACTgtaagttatc ... cgttttgcagTTCTTCATCTTGCTTTCCTGCTCCCTGGCCGTCTTCTGCAACATGAGCC
EST: gi|88754166|gb|DY538307.1|DY538307
EST:     ATCTAAATGGACGGTCATTGTTGAACTACCCTTTTTCGGGAGGGGCAACT                         TTTTTCTTCTTGCTTTCCTGTTCCCTGGCCGTCTTCTGCAACATGAGCCAA
genomic: ATCTAAATGGACGGTCATTGTTGAACTACCCTTTTTCGGGAGGGGCAACTgtaagttatc ... cgttttgcagTTCTTCATCTTGCTTTCCTGCTCCCTGGCCGTCTTCTGCAACATGAGCCAA
EST: gi|20803244|gb|BQ294294.1|BQ294294
EST:     ATCTAAATGGACGGTCATTGTTGAACTACCCTTTTTCGGGAGGGGCAACT                         TTCTTCATCTTGCTTTCCTGCTCCCTGGCCGTCTTCTGCAACATGAGCCAA
genomic: ATCTAAATGGACGGTCATTGTTGAACTACCCTTTTTCGGGAGGGGCAACTgtaagttatc ... cgttttgcagTTCTTCATCTTGCTTTCCTGCTCCCTGGCCGTCTTCTGCAACATGAGCCAA
EST: gi|26456709|gb|CA828292.1|CA828292
EST:     ATCTAAATGGACGGTCATTGTTGAACTACCCTTTTTCGGGAGGGGCAACT                         TTCTTCATCTTGCTTTCCTGCTCCCTGGCCGTCTTCTGCAACATGAGCCAA
genomic: ATCTAAATGGACGGTCATTGTTGAACTACCCTTTTTCGGGAGGGGCAACTgtaagttatc ... cgttttgcagTTCTTCATCTTGCTTTCCTGCTCCCTGGCCGTCTTCTGCAACATGAGCCAA
EST: gi|76282594|gb|DV022162.1|DV022162
EST:     ATCTAAATGGACGGTCATTGTTGAACTACCCTTTTTCGGGAGGGGCAACT                         TTCTTCATCTTGCTTTCCTGCTCCCTGGCCGTCTTCTGCAACATGAGCCAA
genomic: ATCTAAATGGACGGTCATTGTTGAACTACCCTTTTTCGGGAGGGGCAACTgtaagttatc ... cgttttgcagTTCTTCATCTTGCTTTCCTGCTCCCTGGCCGTCTTCTGCAACATGAGCCAA
EST: gi|87155665|gb|DY400454.1|DY400454
EST:     ATCTAAATGGACGGTCATTGTTGAACTACCCTTTTTCGGGAGGGGCAACT                         TTCTTCATCTTGCTTTCCTGCTCCCTGGCCGTCTTCTGCAACATGAGCCAA
genomic: ATCTAAATGGACGGTCATTGTTGAACTACCCTTTTTCGGGAGGGGCAACTgtaagttatc ... cgttttgcagTTCTTCATCTTGCTTTCCTGCTCCCTGGCCGTCTTCTGCAACATGAGCCAA
EST: gi|22935611|gb|BU571886.1|BU571886
EST:     ATCTAAATGGACGGTCATTGTTGAACTACCCTTTTTCGGGAGGGGCAACT                         TTCTTCATCTTGCTTTCCTGCTCCCTGGCCGTCTTCTGCAACATGAGCCAA
genomic: ATCTAAATGGACGGTCATTGTTGAACTACCCTTTTTCGGGAGGGGCAACTgtaagttatc ... cgttttgcagTTCTTCATCTTGCTTTCCTGCTCCCTGGCCGTCTTCTGCAACATGAGCCAA
EST: gi|26560089|gb|CA832324.1|CA832324
EST:     ATCTAAATGGACGGTCATTGTTGAACTACCCTTTTTCGGGAGGGGCAACT                         TTCTTCATCTTGCTTTCCTGCTCCCTGGCCGTCTTCTGCAACATGAGCCAA
genomic: ATCTAAATGGACGGTCATTGTTGAACTACCCTTTTTCGGGAGGGGCAACTgtaagttatc ... cgttttgcagTTCTTCATCTTGCTTTCCTGCTCCCTGGCCGTCTTCTGCAACATGAGCCAA
EST: gi|71444648|gb|DR825698.1|DR825698
EST:     ATCTAAATGGACGGTCATTGTTGAACTACCCTTTTTCGGGAGGGGCAACT                         TTCTTCATCTTGCTTTCCTGCTCCCTGGCCGTCTTCTGCAACATGAGCCAA
genomic: ATCTAAATGGACGGTCATTGTTGAACTACCCTTTTTCGGGAGGGGCAACTgtaagttatc ... cgttttgcagTTCTTCATCTTGCTTTCCTGCTCCCTGGCCGTCTTCTGCAACATGAGCCAA
EST: gi|78120872|gb|DV539256.1|DV539256
EST:     ATCTAAATGGACGGTCATTGTTGAACTACCCTTTTTCGGGAGGGGCAACT                         TTCTTCATCTTGCTTTCCTGCTCCCTGGCCGTCTTCTGCAACATGAGCCAA
genomic: ATCTAAATGGACGGTCATTGTTGAACTACCCTTTTTCGGGAGGGGCAACTgtaagttatc ... cgttttgcagTTCTTCATCTTGCTTTCCTGCTCCCTGGCCGTCTTCTGCAACATGAGCCAA
EST: gi|71444649|gb|DR825699.1|DR825699
EST:     ATCTAAATGGACGGTCATTGTTGAACTACCCTTTTTCGGGAGGGGCAACT                         TTCTTCATCTTGCTTTCCTGCTCCCTGGGCGTCTTTCTGCA-CATGAGCCA
genomic: ATCTAAATGGACGGTCATTGTTGAACTACCCTTTTTCGGGAGGGGCAACTgtaagttatc ... cgttttgcagTTCTTCATCTTGCTTTCCTGCTCCCTGGCCGTCTT-CTGCAACATGAGCCA
EST: gi|78113743|gb|DV532132.1|DV532132
EST:     ATCTAAATGGACGGTCATTGTTGAACTACCCTTTTTCGGGAGGGGCAACT                         TTCTTCATCTTGCTTTCCTGCTCCCTGGCCGTCTTCTGCAACATGAGCCAA
genomic: ATCTAAATGGACGGTCATTGTTGAACTACCCTTTTTCGGGAGGGGCAACTgtaagttatc ... cgttttgcagTTCTTCATCTTGCTTTCCTGCTCCCTGGCCGTCTTCTGCAACATGAGCCAA
EST: gi|78113744|gb|DV532133.1|DV532133
EST:     ATCTAAATGGACGGTCATTGTTGAACTACCCTTTTTCGGGAGGGGAAACT                         TTCTTC-TCTTGGTTTCCTGCTCCCCTGGC-GTCTTCTGCACCATGAGCCA
genomic: ATCTAAATGGACGGTCATTGTTGAACTACCCTTTTTCGGGAGGGGCAACTgtaagttatc ... cgttttgcagTTCTTCATCTTGCTTTCCTGCTCCC-TGGCCGTCTTCTGCAACATGAGCCA
EST: gi|76282593|gb|DV022161.1|DV022161
EST:     ATCTAAATGGACGGTCATTGTTGAACTACCCTTTTTCGGGAGGGGCAACT                         TTCTTCATCTTGCTTTCCTGCTCCCTGGCCGTCTTCTGCAACATGAGCCAA
genomic: ATCTAAATGGACGGTCATTGTTGAACTACCCTTTTTCGGGAGGGGCAACTgtaagttatc ... cgttttgcagTTCTTCATCTTGCTTTCCTGCTCCCTGGCCGTCTTCTGCAACATGAGCCAA
EST: gi|71299090|gb|DR785540.1|DR785540
EST:     TCTAAATGGACGGTCATTGTTGAACTACCCTTTTTTCGG-AGGGGCAATT                         TTCTTCATCTTGCTTTCCTGCTCCCTGGCCGTCT
genomic: TCTAAATGGACGGTCATTGTTGAACTACCCTTTTT-CGGGAGGGGCAACTgtaagttatc ... cgttttgcagTTCTTCATCTTGCTTTCCTGCTCCCTGGCCGTCT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 144

ACCAATCCAGGCAATTTCACTCATTATACTGGGCCCCTTTGTGGACTACTATCTAAATGGACGGTCATTGTTGAACTACCCTTTTTCGGGAGGGGCAACTgtaagttatc ... cgttttgcagTTCTTCATCTTGCTTTCCTGCTCCCTGGCCGTCTTCTGCAACATGAGCCAATACCTCTGCATCGGCCGGTTCTCAGCGACCTCGTTTCAGGTCCTGGGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 278

ACCAATCCAGGCAATTTCACTCATTATACTGGGCCCCTTTGTGGACTACTATCTAAATGGACGGTCATTGTTGAACTACCCTTTTTCGGGAGGGGCAACTgtaagttatc ... cgttttgcagTTCTTCATCTTGCTTTCCTGCTCCCTGGCCGTCTTCTGCAACATGAGCCAATACCTCTGCATCGGCCGGTTCTCAGCGACCTCGTTTCAGGTCCTGGGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 297

ACCAATCCAGGCAATTTCACTCATTATACTGGGCCCCTTTGTGGACTACTATCTAAATGGACGGTCATTGTTGAACTACCCTTTTTCGGGAGGGGCAACTgtaagttatc ... cgttttgcagTTCTTCATCTTGCTTTCCTGCTCCCTGGCCGTCTTCTGCAACATGAGCCAATACCTCTGCATCGGCCGGTTCTCAGCGACCTCGTTTCAGGTCCTGGGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 207

ACCAATCCAGGCAATTTCACTCATTATACTGGGCCCCTTTGTGGACTACTATCTAAATGGACGGTCATTGTTGAACTACCCTTTTTCGGGAGGGGCAACTgtaagttatc ... cgttttgcagTTCTTCATCTTGCTTTCCTGCTCCCTGGCCGTCTTCTGCAACATGAGCCAATACCTCTGCATCGGCCGGTTCTCAGCGACCTCGTTTCAGGTCCTGGGCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattgcagctacaaatgaagttactcattatgctcccttttaaacgttttgcagTTCTTCATCTTGCTTTCCTGCTCCCTGGCCGTCTTCTGCAACATGAGCCAATACCTCTGCATCGGCCGGTTCTCAGCGACCTCGTTTCAGGTCCTGGGCC
 agttgat  putative branch site (score: 207)
                                      ttttaaa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttaatttcttgattgccaaatgtaagcaaaatgtttgtagcagttgattgcagctacaaatgaagttactcattatgctcccttttaaacgttttgcagTTCTTCATCTTGCTTTCCTGCTCCCTGGCCGTCTTCTGCAACATGAGCCAATACCTCTGCATCGGCCGGTTCTCAGCGACCTCGTTTCAGGTCCTGGGCC

- - - - - tgattgc
- - - - - - - - - - - - aagcaaa
- - - - - - - - - - - - - - - - tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - ctacaaa